Magnetic nanoparticles have gained significant attention as a therapeutic agent for cancer treatment. Herein, we developed chitosan oligosaccharide-stabilized ferrimagnetic iron oxide nanocubes (Chito-FIONs) as an effective heat nanomediator for cancer hyperthermia. Dynamic light scattering and transmission electron microscopic analyses revealed that Chito-FIONs were composed of multiple 30-nm-sized FIONs encapsulated by a chitosan polymer shell. Multiple FIONs in an interior increased the total magnetic moments, which leads to localized accumulation under an applied magnetic field. Chito-FIONs also exhibited superior magnetic heating ability with a high specific loss power value (2614 W/g) compared with commercial superparamagnetic Feridex nanoparticles (83 W/g). The magnetically guided Chito-FIONs successfully eradicated target cancer cells through caspase-mediated apoptosis. Furthermore, Chito-FIONs showed excellent antitumor efficacy on an animal tumor model without any severe toxicity.